The Heart of Darkness
by x Varda x
Summary: Complete!The team go off-world where something happens to McKay,causing him to act strangely.Can Sheppard figure out what it is and save his friend before it’s too late? Will McKay be able to survive for long enough to prevent the destruction of Atlantis?
1. The Brink of Darkness

Disclaimer - "Stargate" and all related characters are the property of MGM Television Entertainment. I just like to mess with them in the universe they created!

Rating – T

Set in Season 3, just after 'McKay and Mrs Miller' – but there are no spoilers for any episodes

**Chapter 1 - The Brink of Darkness**

Sheppard parked the Jumper a short distance away from the energy reading they were going to investigate. He took point as he walked along the rear hatch and out into the rock-strewn landscape.

Wind blew along the ground and tossed dust up into the air around his feet. He looked up at the cliff a short distance away and noted there were some scrubby plants tenaciously growing from the face and a large rockfall at the ground.

He heard a harsh and exaggerated coughing behind him and spun around to watch Rodney as he covered his mouth and held his nose with his hand, "Are you sure it's safe Sheppard? I can't breathe," he muttered nasally.

John frowned and rolled his eyes, "Come on McKay. It's fine."

Ronon and Teyla followed behind and also peered warily around at the apocalyptic landscape. They were in a dry canyon surrounded by grey and dark brown walls of rock. A weak sun shone onto the tops of the cliff on one side. No light was able to reach the bottom where the team were, so they were left shrouded in shadows.

Sheppard looked at the rest of his team and shrugged, "Okay let's head out. Ronon take point, Teyla you've got our six."

The Satedan nodded and walked in the direction of the fairly obvious artificial structure several hundred metres away.

Sheppard hung back and stood closer to Rodney. He kept his eyes sharp for any dangers while the scientist stared at the scanner and angled his head down.

Another gust blew through the canyon and howled against their ears and made walking difficult for a while. Sheppard narrowed his eyes, but grit still got inside, making them water.

Beside him, Rodney started coughing again, a little more naturally this time. The scientist started going through all the pockets on his tac vest, but came up short. "I swear I'm going to insist on face masks and goggles being standard equipment in these things."

Sheppard smiled and blinked to clear his vision. He patted Rodney on the back, "I'll see what I can do when we get back. Just don't breathe too deeply if it's bothering you."

Rodney gave him a petulant look and shook his head as he went back to studying the tiny screen in his hand.

Sheppard turned around and looked at Teyla a short distance behind them. Her face was pinched together in poorly concealed amusement and her hair was full of dust making it a much lighter brown than normal.

Ronon kept ploughing ahead with his blaster in hand; ready to shoot anything that may try to attack. He seemed to be ignoring the conversation behind him.

Five minutes later they stood in front of the building they had seen on the sensors. Sheppard watched over Rodney as the scientist walked around the edge of the wall and frowned down at the scanner.

The building was only one storey high and dark brown like the rest of the canyon. One half had been on the losing side to a battle with a rockfall and it was completely buried.

Sheppard gazed at the pile of sloping rubble briefly and wondered if the building underneath was crushed. He then looked back at Rodney, who was watching him and smiling.

The scientist waved the scanner in front of him so that Sheppard could see the screen. But the movement made it impossible to read anything, so John just raised his eyebrows at McKay.

Rodney's face fell a little and he sighed before he spoke, "Massive power reading." He said it in an incredulous way; almost like it had been so obvious he could not believe Sheppard had not been able to figure it out.

Teyla kept lookout over the canyon and said, "How massive? Could there be a ZPM here?"

Rodney waved his hands about in paroxysms of delight and his face lit up again, "The power reading is certainly high enough!" He gazed at the building dreamily.

Sheppard found himself infected with Rodney's enthusiasm and grinned as he watched the happy expression on McKay's face. He could imagine that the man was now thinking about all the things they could now do if they found a ZPM. The city had been without one for several weeks and Sheppard had to admit that he found it hard to sleep sometimes, knowing that they would have no shield or cloak if the Wraith showed up again.

The corners of Ronon's mouth were also twitching up into a smile when Sheppard looked over at him.

Rodney shook his head after a moment and walked over to the blank wall. Sheppard frowned; he did not like it when the scientist tried to break away from their protection. He rushed over, "Rodney?"

The scientist touched the wall briefly and said, "Ah ha!" when a panel slid back to reveal a small switch.

"Rodney wait a moment!" Sheppard said, but before Rodney heard him, he had already pressed the button.

Sheppard raised his gun and pointed it at the door, which suddenly slid open in front of Rodney.

John ran over before Rodney could step through the doorway. The scientist had already begun to walk over to it. Sheppard put a hand on McKay's chest to stop him going in first and got an indignant, "Hey!" for his trouble.

Sheppard gave him a warning look and peered into the open doorway. He flipped the light on his P90 and said, "Teyla stay out here, Ronon, you're with us."

Sheppard heard Ronon approach behind him and another small squawk in protest from McKay.

John then walked through the door into the building.

* * *

Sheppard shone the light on his gun all around the room they stepped into. Ronon came in next and stood next to the Colonel.

One side of the room had been crushed by the debris from the cliff which had landed on it. Twisted and distorted metal slanted down one of the walls and in some places the wall had been completely breached and pebbles and dust were heaped on the floor.

Sheppard walked further into the room and noticed several panels and dirt-covered Ancient consoles what had probably been in the centre of the room, but now was right next to the damaged section.

Ronon went to the other side of the room.

Sheppard turned back to the door just as a sarcastic voice echoed around the room, "So Colonel is it safe enough for small children or must I stand out here and get suffocated by the tiny shards of rock when they get blown into the air again?"

Sheppard saw Ronon rolling his eyes, but he found himself smiling, "Yes it's fine."

Rodney almost ran into the room himself, but his eyes glanced around nervously when he noticed the debris and he slowed to a fast walk to avoid slipping.

Sheppard watched as he unhooked the tablet from his back and plugged it into one of the consoles. He muttered under his breath and started typing.

"Ah yes, here we go."

Sheppard blinked as the light in the room activated when Rodney powered up some of the systems. He could see the dust in the air through the beams of light now illuminating it.

Sheppard watched Rodney as he began to press the panels on the Ancient console directly. He then looked at Ronon, who was staring at the damaged wall as if it might fall down or explode inwards at any moment.

Suddenly there was a sharp intake of breath from Rodney and he fell over with a small pained cry as he went down with a crash.

Sheppard could not see him for a moment over the tops of the consoles. He rushed over and found Rodney sprawled on the floor with a hand pressing firmly against his chest and his brow furrowed.

John crouched down next to him and Ronon stood over them both. "You alright McKay?" Ronon asked

Rodney looked up at him and muttered, "What?"

Sheppard frowned at the scientist's confusion, "He said are you alright?"

Rodney gave a small gasp and closed his eyes, all the time pressing his clawed hand more tightly over his heart so that his fingertips went white.

"Rodney?" Sheppard asked in concern.

The scientist looked up at him and his pale and frightened face was not lost on Sheppard, "Uh… yes… yes I'm fine. I…I just tripped."

Sheppard narrowed his eyes and helped the man up when he finally released the grip on his chest and held his hand up for Sheppard to grasp.

Sheppard watched as Rodney leaned heavily against the console and took a few shaky breaths. He seemed to be deep in thought about something and Sheppard asked quietly, "Are you _sure_ you're alright. We could head back and ask Beckett to check you over."

Rodney hissed and snapped, "I'm fine, Colonel. How many times do you have to be told?"

Ronon was now frowning at the strange outburst, "Did you find a ZPM?"

That seemed to work McKay up even more and his eyes darted from side to side in an unnerving way. Sheppard went over and grabbed his shoulder.

"No!" Rodney cried as Sheppard touched him.

John quickly drew his hand back like he had been burned, "What?"

Rodney looked up at him and spoke quickly, "I mean, no, I didn't find a ZPM. There is a large power source coming from below the surface though. I think it would be better if I take the data back to Atlantis for further study and bring a larger science team back at a later date."

Sheppard preferred the idea of getting Rodney back to Atlantis to be checked. After the strange things he had just witnessed he had no argument, "Sounds good. Let's head back."

Ronon and Sheppard locked eyes and shared a meaningful look for a moment behind McKay's back. The Satedan nodded in agreement.

* * *

Sheppard grew even more worried when McKay stayed strangely mute as they walked back to the Jumper. His breath would sometimes hitch as if in pain, but when John rushed over to him, he would be given a weak smile, but no words ever left the scientist's lips.

When they were settled in the Jumper and airborne back to the gate, Sheppard turned to look at Rodney and found his face had a fixed grimace and he was holding the sides of his seat tightly.

"Rodney?" There was no reply.

Teyla leaned forwards and grabbed McKay's shoulder. She easily spun him around in the chair and Sheppard also turned so that they were all facing the centre of the cockpit.

Rodney looked up at Sheppard with a fearful expression and Teyla frowned, "Rodney, what is wrong? You have been different since you left the building with the others."

He stuttered as he spoke, "I told you I'm fine. Just a little tired that's all."

"What about the ZPM?" Ronon asked.

"No…not sure whether there was…is a ZPM anymore. Need to send a science team back, yes."

His unsteady speech was utterly disconcerting to Sheppard who just nodded sadly and turned back to monitor the flight.

Sheppard saw Rodney flinch and close his eyes when Ronon patted him on the back after they were turned in the correct direction in their seats once more.

He shook his head in confusion and pushed the Jumper for more speed to get back to Atlantis.

* * *

Sheppard's frown deepened after he heard Beckett's report on Rodney after the mandatory check up on all of them after going off-world.

"There's nothing wrong with him, if that's what you're asking Colonel. His blood pressure and heart rate are a wee bit high, but other than that he's in perfect health. Well as perfect as he usually is, being Rodney."

Sheppard sighed, "If you say so. I still don't think he's fine though."

Carson shook his head, "Well there's nothing medically wrong with him."

Sheppard nodded and walked over to Rodney who was rolling his sleeve back down and glaring daggers at the nurse as she walked away to analyse his blood sample.

He saw the Colonel approaching from the other side of the room and quickly got up and left the infirmary. Sheppard chased after him, but he must have been walking really quickly or possibly even running as he was nowhere to be seen when Sheppard stepped out into the corridor outside the infirmary.

He frowned in frustration. He just hoped that Rodney would find the courage to speak with him about what was bothering him. He liked to think that McKay could confide in him about a problem, so he decided he would give the scientist a few hours before starting to force the issue.

* * *

Sheppard kept himself busy over the course of the afternoon. He went to the gym, sparred with Ronon and oversaw a training session in the shooting range.

He glanced at his watch and noted that he had a half hour break before his allocated time for writing up the mission report from that morning. He had still heard nothing from Rodney and his heart sank in worry.

He reached up and tapped his radio, "Sheppard to McKay."

There was a long and tense silence before a timid voice answered, _"Go ahead."_

"Where are you?"

The radio cut out for a few seconds and Sheppard frowned. He decided to head in the direction of the science lab, as that was usually where Rodney could be found. He tapped the radio again, "McKay?"

An even quieter voice answered, _"I'm in the lab."_

The radio then cut out again and Sheppard nearly ran to get to the transporter and find out what was going on.

Two minutes later, Sheppard entered the science lab and found Rodney hunched over the desk with a red face and looking like he had just run a marathon.

Two other scientists were in the lab with him typing away on computers on the other side of the room with their backs to Rodney. Sheppard could not recall their names.

Rodney straightened up and winced as Sheppard came closer. He took off his headset and tossed it onto the table, while muttering, "Sorry about that. I think there's something wrong with it."

Sheppard looked the scientist up and down and frowned when he noticed the gun strapped to the man's leg. He pointed down at it, "Why've you got that?"

"I…uh…" he wrung his hands together nervously and his eyes darted around the room in panic, "I forgot to take it off after we got back from the mission."

"Well you don't need it now," Sheppard said and held out his hand.

Rodney stood up and gasped as he slowly unclipped the belt and handed the gun to Sheppard.

"What's wrong with you McKay? You've been acting strangely ever since we left that lab."

"N-nothing! I'm just a little tired, like I said earlier."

Sheppard was still not buying it and Rodney saw it too, so he continued to speak, "Listen John, I've got a lot of work to do. I assure you there's nothing wrong and if there was, you know I'm always the first one to go to the infirmary straight away."

Sheppard nodded slowly, wishing he could believe what Rodney was saying. There was something about McKay's obvious discomfort as he stood there that was gnawing away at Sheppard and making alarm bells ring. He decided to give Rodney the benefit of the doubt.

"Alright Rodney, but if you don't join us for dinner at 6pm I'm calling Carson."

Rodney gave him a brave and grim smile, which Sheppard returned even though the expression made him feel even more concern for the scientist than he had done previously.

He walked out to head back to his quarters so that he could pick up a computer for his write-up. He turned in the doorway to the science lab and frowned when he saw Rodney holding his back and grimacing as he sat back down in the chair slowly.

* * *

It had only been thirty minutes since John had left Rodney in the science lab when his radio buzzed.

"_Sh-Sheppard?"_

He looked up from his computer as he sat in the Mess Hall and stopped typing.

"Go ahead McKay."

_"John… I… I…"_

Sheppard frowned and stood up quickly.

"Rodney? What is it?" He just wished McKay would say something about what was going on.

"_I'm in the Jumper Bay."_ He blurted out in stark contrast to his previous stuttering speech.

There was a high-pitched cry of pain over the channel and then the radio cut out.

Sheppard tapped his radio as he ran out of the Mess Hall to the transporter, "Sheppard to Major Lorne. Meet me in the Jumper Bay STAT."

Sheppard was halfway to the transporter when his radio activated again, _"Dr Weir to Colonel Sheppard."_

He frowned in confusion, "This is Sheppard."

_"We've just detected an unauthorised Puddle Jumper launch. It's currently hovering close to the Gate Room and we have been unable to contact the occupants."_

_Occupants? Who else was with Rodney?_ "I'm heading to the Jumper Bay now, something's going on with McKay. I was going to meet him up there."

Weir said, _"There are three lifesigns on board the Jumper and we'd feel much safer if it wasn't so close to the Tower,"_ she paused before she said diplomatically, _"Do what you can."_

"Understood." Sheppard said, praying it would not come to that.

* * *

Sheppard met Major Lorne in the Jumper Bay a couple of minutes later.

The Major nodded, "Colonel. Dr Weir has informed me of the situation. Do you think Dr McKay's flying the Jumper?"

Sheppard said, "I don't know, but it seems likely based on what he said."

He looked around the Bay and then turned to Lorne, "Fly my wing. Let's see what's going on."

The Major nodded and they both went into separate Jumpers and flew up out of the Bay into the sunlight sky of Lantea.

Sheppard brought up the HUD and immediately saw the solitary Jumper still hovering by the Tower. As he watched, the craft twitched slightly and turned to face the incoming Jumpers he and Lorne were flying.

Sheppard suddenly noticed there were only two life signs on the other Jumper and it made his heart skip a beat. He hoped he had misheard Elizabeth when she said there were three life signs on the craft.

He studied the readings in more detail and saw that out of the two life signs, one was getting weaker all the time while he watched. The small light fading from the screen steadily.

He opened a channel to the other Jumper and rigged it so that the Gate Room and Major Lorne could also hear.

"Colonel Sheppard to Jumper Ten."

There was no reply.

Suddenly two drones shot out of the other Jumper.

"Lorne, break right!" Sheppard ordered over the radio.

_"Acknowledged."_

Sheppard rolled the Jumper and flew it on full burn as he dodged around the single drone which tracked after him. He weaved in between the buildings and towers of Atlantis as he tried to shake off the drone.

He was just getting into a rhythm, when the drone suddenly lost power and fell from the sky to splash into the sea below.

Sheppard frowned, "Lorne?"

_"I know Sir, it happened to me too. It just stopped, I don't understand it."_

"Nor do I Major. Converge on Jumper Ten."

_"Understood."_

The craft was still hovering malevolently in its previous position. Sheppard watched the HUD and noted the two life signs were still on board. The radio channel was still fully open so that the people on the hostile Jumper could hear everything. _If they're listening_, Sheppard thought sadly.

He was just about to try and speak with Rodney, when another drone shot out from the craft. It headed straight and true towards the Gate Room.

Sheppard's eyes widened in shock and he did the only thing he could think of.

He channelled as much power as possible to the shields and intercepted the drone.

The resulting explosion strained the inertial dampeners too much and Sheppard was thrown roughly around in his chair. He managed to stay upright, but saw that the shield had been completely drained.

"_Colonel?"_ Elizabeth asked in concern.

"I'm fine, but I don't think I'll be doing that again in a hurry."

He switched off the radio link with the other Jumper so that he could just speak with Lorne and the Gate Room.

Sheppard steeled himself before he spoke, "Major…"

To his surprise Lorne cut him off, _"I know Colonel. But it's acting as an enemy ship. We don't have a choice."_

Dr Weir said, _"But if Rodney's on board, you'll kill him."_

Sheppard furrowed his brow in sadness, "Don't…I think I may be able to disable the Jumper without destroying it."

Lorne said,_ "If you don't he could destroy the Gate Room and everyone inside."_

Sheppard knew he had to act fast as another drone could launch from the other Jumper at any time. As much as it pained him, Lorne was right, the Jumper and whoever was on board had to be stopped.

He closed his eyes and took a deep breath. When he snapped them open he fired a single drone towards the stationary Jumper.

He detonated the drone close to the engines with a thought and a huge explosion tore through the pod, breaking it away and making the Jumper spin down slowly and out of control towards the ocean.

As he watched the other engine cut out too and the descent speed increased.

"Lorne! Grapple!"

Lorne's Jumper flew over and the grapple shot out. It missed the stricken craft by several metres and Sheppard heard the Major curse over the radio. Sheppard knew there was only one more chance or the Jumper and its occupants would be claimed by the ocean. With the hull likely to have been breached they would drown.

_If there's anyone left alive to be drowned_, Sheppard thought as he sped after the rotating craft.

He gritted his teeth and lined up the shot.

He fired the grapple and the thin thread flew out rapidly from under the hull as Sheppard looked out of the window and held his breath.

The grapple thudded into the rear hatch of the other Jumper just before it hit the water and Sheppard sighed in relief, but he knew it was not yet over.

"_My grapple's reset."_ Lorne said.

"Help me out."

Lorne obeyed and now that the other Jumper was not moving so rapidly he did not miss.

The other Jumper swung around wildly under the grapple lines and Sheppard could not move it fast enough to avoid it from smacking into a building as he moved his craft over to one of the piers with Lorne to lay the damaged Jumper down on relatively flat ground.

He winced when he imagined what it would have been like to be shaken around inside a Jumper like that. He could almost hear snapping bones. He tried to block the thoughts from his mind as he carefully rested and released the Jumper onto the surface of the pier.

Sheppard and Lorne both deactivated the grapple lines and Sheppard noticed there was still one very faint life sign on the HUD.

"Son of a…" he muttered, "We need a medical team to meet us on the South Pier."

Both of the fully functioning Jumpers landed next to the one they had just shot down as a small plume of smoke leaked out from the wreckage and rose into the Lantean sky above.

* * *

TBC


	2. The Heart of Darkness

Now from the other POV…

**Chapter 2 – The Heart of Darkness**

Rodney walked into the Ancient building and headed straight over to a console. He trotted eagerly to start with, but his feet slid on the pebbles beneath them so he decided to slow down rather than fall over. He glanced at the collapsed wall in fear, but reasoned that it may have been like that for ten thousand years and another few hours hopefully would not cause it to cave in any further.

He hated how dry and irritated his throat was from the lungful of dust he inhaled a few minutes ago. He had already drunk nearly half a bottle of water while he waited for the all clear from Ronon and Sheppard, but he was still struggling not to cough as he stepped inside the dusty room.

Plugging his tablet into the most likely looking console, he typed away and studied the data. He quickly found the basic systems and said, "Ah yes, here we go."

The lights came on and Rodney continued to tap on the screen for a few moments. He suddenly spotted the source of the energy reading and found it strange that it seemed to be coming from directly underneath the console he was using.

He thought it odd that the Ancients, in their wisdom, had not concealed it in a better location. The ZPM room on Atlantis was huge and well shielded, but to bury one in a console seemed strange to him.

He decided to go straight into the system and use the console directly.

Rodney pressed a couple of the panels and shivered as he felt an unusual sensation flowing up his arms and collecting in the centre of his chest.

He drew in a noisy breath as he stopped hitting the panels and lifted his hands up. The icy feeling which was pooling at his core continued to increase. He was just about to say something, perhaps that he was no feeling very well, when the cold turned to pain as something burrowed into him and gathered around his heart.

He cried out and put his hand over the source of the hurt. The next thing he knew the room spun around in an unsteady fashion and then tipped as he fell down.

The agony in his chest increased as he lay there and he wondered whether he was having a heart attack. It seemed to consume his whole being and tremors of pain spread out from the focal point and ran down his arms and legs.

He increased the pressure with his hand on the left side of his chest and wished the touch could soothe away the agony beneath or just make it stop.

"Are you alright McKay?" He heard Ronon ask dimly from high above him.

Just as the pain had started, it suddenly vanished. Rodney was still filled with the memory of it and he was puzzled as to what had just happened. He was about to answer when he heard a terrifying sound in his head.

**Say you tripped.**

The voice was a low and unemotional monotone. He could not tell whether it was male or female.

Rodney stuttered, "What?"

Sheppard spoke in concern, "He said are you alright? Rodney?"

**Say you tripped or we will kill you.**

Another squeeze of his heart made Rodney gasp and close his eyes again. The sensation left him once more and he gazed up at Sheppard. He tried not to shudder as he lay there and he had no desire to die, so he obeyed the voice.

"Uh… yes… yes I'm fine. I…I just tripped." His voice was more hesitant than he expected and he braced himself for the killing blow. When it did not come he thought he must have succeeded in placating the thing that had spoken to him.

**Make no sign that you can hear us or we will make the last moments of your life **_**very**_** unpleasant for you.**

Rodney finally released the grip over his heart and let Sheppard help him to stand. He drew in a couple of deep breaths and leaned on the console so that he did not fall over again.

**Make an excuse to leave the planet and head back to Atlantis. We will be watching.**

Rodney thought that whatever was in him may be contagious or would pass out of him if he were to be touched, as it had emanated from the control panel. When he looked up Sheppard and Ronon were still staring at him.

Sheppard asked, "Are you _sure_ you're alright. We could head back and ask Beckett to check you over."

"I'm fine, Colonel. How many times do you have to be told?" The stress at having to lie to his friend in order to stay alive annoyed Rodney more than he could ever admit. It made his words came out more harshly than he had intended and it hurt him more deeply because he was speaking to someone who was showing genuine concern for his welfare.

Ronon asked, "Did you find a ZPM?"

Rodney's mind worked as fast as he could make it to come up with a suitable lie to tell his team mates so that they could get out of there. Maybe he could get Carson to scan him and find out what was going on. A tiny flicker of hope began to spread through his mind from the thoughts about Dr Beckett and being safely in the hands of people who could help him.

Before he could speak he felt a hand on his shoulder and realised that Sheppard was touching him.

He cried, "No!"

Rodney just hoped that his theory about transferring the being was incorrect, if not then it was too late for John as well.

Sheppard looked hurt at the outburst and asked, "What?"

Rodney's quick thinking came into play as he spun his yarn, "I mean, no, I didn't find a ZPM. There is a large power source coming from below the surface though. I think it would be better if I take the data back to Atlantis for further study and bring a larger science team back at a later date."

Although truthfully, Rodney doubted there was anything in the lab at all.

Luckily for Rodney, Sheppard seemed to buy it and said, "Sounds good. Let's head back."

* * *

The walk back to the Jumper was tortuous for Rodney. He wondered at every moment whether he was going to feel another crush in his chest which would hurt as much as it had done in the Ancient building. The memory of the pain still fresh in his mind did not help to alleviate his fears, but just to intensify them as he tried to think about something else.

Rodney considered typing something on his tablet to show Sheppard or perhaps telling him what had happened.

He opened his mouth to speak, but was cut off.

**Do not say a word.**

The return of the voice was punctuated with a small amount of pressure in Rodney's chest, which made his heart seem to skip a beat as his breathing hitched.

_So you can hear what I'm thinking too?_

**Yes, we can hear everything and we see right through you Dr McKay.**

_What's your name? What shall I call you?_

**We have no name.**

_How about Heart Attack Harry?_

**That is very silly Dr McKay.**

_Just Harry then, or perhaps Harpy would be more fitting, as you seem to have your claws embedded in me?_

**You are a truly irritating man Dr McKay and some of us are beginning to think that it would be better just to kill you now rather than have to endure. Even if it means our plan will not succeed.**

As the voice continued to drone on, the pressing grip around Rodney's heart increased and his breath caught again.

_No no no! Don't kill me! And what 'plan?'_

The circle of pain loosened but did not diminish. Sheppard had rushed over to Rodney's side when he heard the difficulty he had breathing.

The scientist gave him as brave a smile as he could muster, but found that he could not speak as it hurt him to have to lie to his friend in order to stay alive.

**You will see Dr McKay, if you can hold your tongue for long enough.**

Rodney did not think that he had any other choice so he followed the others into the Jumper and sat down with a sigh.

He held onto the seat tightly and grimaced, grateful for any kind of outlet for his agony when the pain in his chest returned, just to remind him that it was still there.

He even managed to fob off his team when they asked him what the problem was. He winced when he realised that the whole team had now touched him and if the being was contagious they were all now infected. He prayed that it was not.

* * *

Carson stood next to Rodney as he sat on the edge of one of the beds in the infirmary for his post mission medical check.

McKay looked up and asked, "Did you find anything?" His voice had a slight pleading quality to it, which unnerved Carson no end.

He sighed before he spoke, "I want you to take it easy for the rest of the day Rodney. You're blood pressure and heart rate are too high for my liking, but not at dangerous levels. Otherwise there's nothing wrong with you."

Rodney's face fell and he looked down at his feet as he mumbled, "Can I have a full scan?"

"That's not standard procedure Rodney."

"I know but… uh… humour me ok?"

**He will not find anything.**

Rodney flinched at the return of the voice and Carson shook his head as he sighed.

Rodney was not going to give up so easily so he kept pressing, "What about a blood test then?"

Carson frowned, "Well that _is_ strange for you. Volunteering for needles, I think there must be something wrong."

**Again, we already know he will not find anything.**

Carson walked away and spoke to a nurse, who came over to Rodney. He hastily rolled up his sleeve and she found a vein.

Rodney tried not to wince as she punctured his skin with the needle and drew blood from the inside of his elbow.

**That is very cowardly Dr McKay, such a massive reaction to so small a hurt. You really are weak aren't you? Perhaps we will need to try something else to persuade you.**

_Persuade me?_ Rodney thought in panic.

Before the voice could answer, he saw Sheppard coming over to him. He did not feel up to a confrontation with the Colonel over his health at the moment, so he shoved his sleeve back down, grabbed his tablet from the corner of the bed and walked out of the infirmary.

When he reached the corridor, he ran as fast as he could.

* * *

Rodney went down to his lab so that he could attempt to lose himself in some work and avoid thoughts of pain and death, which constantly assailed him as he ran.

He stopped a short distance away from the door and doubled over to get his breath back. When he was sufficiently recovered he breezed into the lab as nonchalantly as he could.

He gazed around the room and saw that there were two other members of his science team typing on laptops, a man and a woman. They tipped their heads to him as he entered the room and went back to what they were working on.

Rodney relaxed a little at the familiar surroundings. He knew that he would just have to wait for the results of his blood test and then everything would be alright.

He sat down in a spare chair on the opposite side of the table to the other two people. Their names eluded him completely for a moment, which was not surprising as he was always too wrapped up in his latest project to actually get to know his staff. He thought they had been part of the recent batch to arrive from the Daedalus a few days ago. He sifted through his thoughts and the names Dr Evans and Dr Silvestro surfaced.

He pulled the laptop over and started to upload the data from the mission from his tablet.

While he waited for the process to finish he thought about the rest of his team and hoped they had not been infected through the contact they had made with him.

Suddenly the female scientist, Dr Silvestro, looked up, "**Oh but we do not just spread through contact Dr McKay**," she said in a scary and even monotone.

Rodney's heart pounded against his ribs in panic.

The man, Dr Evans, also lifted his gaze from the computer and stopped typing, "What the hell? What…" he twitched a little and his eyes rolled before he spoke again, "**There is nowhere you can go now where you will be safe from us**."

"What's the matter, lost your nerve?" Rodney said fearfully, "What happened to all the heart attack inducing pain you were inflicting on me?"

**We are no longer able to damage you directly, so we needed to gain control over others to enact our mission.**

The scientists gazed vacantly back at Rodney as he listened to the voice in his head.

He spoke out loud anyway, "You seem to be able to control them, so why not me?"

Silvestro started, **"You have the Ancient gene which…"**

Evans continued the sentence and Rodney's eyes skipped between them in fright, **"…makes it impossible for us to control you directly. It is…"**

The voice continued in Rodney's head.

…**blocking our attempts somehow. But we need someone with the gene for the success of our mission.**

Rodney had had enough of the vacant gazes from the two scientists facing him and he pushed himself out of the chair. If he was in danger he would need something to defend himself. He knew he would not be able to go to Sheppard, Ronon and Teyla with his problem as they may have been compromised.

He thought about Sheppard for a moment, another gene carrier would be able to resist the influence and he felt relief that he had thought of the way out of the situation. He walked out of the lab and headed down the corridor.

**He will be dead before you reach him if you say anything. We now control people all over the city. Nothing you do can stop us.**

Rodney halted in his tracks and grimaced. He still needed some form of protection so he turned around and headed to his quarters. He wondered whether the beings were bluffing, he sincerely hoped they were, but could not take that risk.

* * *

Rodney grabbed the gun he kept hidden in his desk, strapped the belt around his waist and secured it to his leg with the other clips. He kept it there in case they were attacked in the night and he was asleep in his quarters.

He felt a little calmer with the reassuring weight of the weapon against his thigh.

He walked into the bathroom and looked at himself in the mirror. He knew he was pale, but the face he saw was quite unlike what he was used to seeing gazing back at him when he studied his reflection, even after an all nighter.

He lifted up his shirt and examined his chest for signs of damage caused by the pain he had felt. His skin was as pale as his face and he frowned when he saw no marks. He ran his hand over his chest and could not feel anything unusual either. He let his shirt drop back down and took one last look at himself and grimaced before he walked away and out of his quarters.

As he walked along the corridor, Rodney kept his head down and did not look at anyone as they walked past. He half expected to be assaulted at any moment by a possessed member of the expedition.

He decided to go back to the science lab and hoped that Sheppard would eventually come to see him on his own.

When he reached the lab, Rodney's heart sank when he saw the two scientists were still there. There was no courteous nod to him this time, but they did look up as he entered. Their empty eyes filled Rodney with fear and he sat down at the laptop again to analyse the data which was now uploaded.

The more Rodney read, the lower his heart sank. He saw frighteningly familiar codes sequences and he desperately tried to find another explanation, because he knew that it would not just be him in trouble if it were true. The more he studied the data, the more his fears were confirmed. In hindsight, he wished that he had spent more time looking at the data back on the planet, then he would never have touched the panel.

After a few hours of reviewing the data, he finished the analysis and muttered under his breath, "Replicators. We're so screwed."

**Replicators? We can see in your mind that you call the Asurans the Replicators. How very astute of you to figure out who we are.**

Rodney looked over at the two scientists who had started to watch him as he reached the conclusion of his findings.

Evans spoke, **"We may as well tell you our intentions as there is nothing you can do about it anyway now."**

"That would be nice." Rodney said sarcastically and folded his arms over his chest protectively as he leaned back in his seat.

Silvestro started, **"We knew of your existence after you found our planet."**

Evans said, **"So we created a nanovirus programmed with the powerful AI of several Asurans. We attached it to a false power reading we knew you would be drawn to."**

Rodney looked down as the voice continued in his mind.

**The trap was sprung and you fell in as predictably as we had hoped. This city must be destroyed.**

"You want to destroy Atlantis? But there's nothing you can do. We don't have a ZPM to overload."

Evans said in the even and disconcerting monotonous drone, "**We realise that now, but it does not mean we cannot inflict as much damage as possible."**

Rodney was about to speak when his radio activated, _"Sheppard to McKay."_

**If you say anything he is as good as dead and so are you.**

Rodney's chest constricted in panic and made it hard to breathe, "Go ahead."

Evans and Silvestro both got up out of their chairs and came over to hover malevolently behind Rodney.

"_Where are you?"_

Rodney deactivated his radio and turned in his seat to face the scientists looking down at him vacantly. He held his hands up in surrender, "I have to answer him! He probably knows where I am anyway. There's nothing I can do!"

The Replicators did not answer and Sheppard's voice came over his radio again, _"McKay?"_

There was still no monotone voice to offer guidance over what he should or should not do so he said, "I'm in the lab."

He instantly regretted it though, as Evans reached forwards and tore the headset from his ear. She turned it off and tossed it onto the desk.

Rodney stood up to try and square up with the scientists who were now threatening him. He wondered exactly how much control the nanovirus had over them and what they were going to do now that he had disobeyed their instructions.

**You should not have done that Dr McKay.**

Evans and Silvestro advanced on him and Rodney backed up. They were blocking his path to the door so there was no escape for him when Evans grabbed his shoulders and pushed him with a strength Rodney did not believe was natural.

He fell over and slid along the floor at an alarming speed. His movement was suddenly stopped and he grunted in pain when his back slammed into the leg of a desk.

Silvestro and Evans kept walking over to him and Silvestro crouched down and hauled him to his feet.

Rodney tried to shake off the grip and winced as his bruised back wrenched. He considered kicking out, but knew that there were still people underneath the nanovirus control and he could not do it.

Silvestro went behind Rodney and grabbed his hands. She pulled them back against his struggling and pinned them behind him so that Rodney could not move.

Evans brought his fist back and drove a savage punch into Rodney's stomach, making him cough and close his eyes as he tried to double over.

Silvestro still held him in a death grip and he could not even free his arms to protect himself.

He kept his eyes firmly glued shut and muttered, "Sh-Sheppard." He furrowed his brow and coughed again.

**You are right. He is coming. Sit at your desk and act like there is nothing wrong.**

Silvestro released Rodney's arms and he swayed as he clamped them across his midsection and bent over at the waist to get his breath back.

He looked up at Evans who was still looming over him, **"If you try anything…"** He reached behind his back and drew out a sharp knife.

Rodney's eyes widened as the light in the lab glinted off the blade and into his face.

He nodded and winced as he walked over to his seat and sat down. He picked up his headset and placed it behind his ear just as Sheppard walked in.

Rodney's conversation with Sheppard was forced and uncomfortable. He was not helped by the tingling sensation in his belly where he had just been hit, which occasionally burst into pain and made him wince involuntarily. He could also feel sore bruises across his back protesting whenever he turned.

He begrudged the loss of the gun as Sheppard took it from him, but he knew he never would have had the nerve to use it against any of his colleagues, no matter how badly they threatened or hurt him.

He did not like the way the two scientists pretended to work and then stopped typing to listen as Rodney came closer to revealing the truth to Sheppard. He so desperately wanted to tell John what was going on, but he knew his own life would be forfeit along with many others if he said anything.

When Sheppard walked away, Rodney sat back down in his chair and tried to think of a way out of the situation he was in. He drew a complete blank and decided it would be better just to see how things played out. He considered running from the lab and hiding, but that would only prove how cowardly he was, so he stayed put.

**That is very wise Dr McKay. After all, you know there is nowhere you can go where you are safe from us. You are also about to find out what our revised plan is.**

Evans and Silvestro got up from their chairs on the other side of the lab and walked menacingly over to Rodney. Silvestro stopped at a cabinet and grabbed a roll of duct tape before she continued. Their blank stares filled him with dread and he stood up to face them head-on.

As they drew up level with him, Evans grabbed the knife again and pointed the tip of the blade at Rodney. He said, **"Move,"** and once again concealed the knife as McKay did what he was told.

* * *

TBC


	3. Unbreakable

T bordering M and a lot darker than my usual fare…

**Chapter 3 – Unbreakable**

Rodney walked down the corridor with Dr Evans and Dr Silvestro behind him. He could almost feel their vacant eyes boring into his back as he proceeded.

If he faltered or tried to stop, he would feel a hand pushing his back, right where the bruise was and it made him hiss and continue.

He had no idea where he was being led, but he knew he had to get away.

**Do not try anything or it will be more than a hand you feel in your back next time.**

Rodney decided enough was enough and as both his captors were walking behind him he would be able to run in an attempt to get away from them.

He ran as fast as his damaged muscles would allow and turned his head to look back after he rounded a corner. He saw that he was not being followed and decided that the Gate Room would be the safest place to go.

When Rodney turned his head round to look where he was going, he saw a marine in front of him and he could not stop in time to avoid the outstretched fist which hammered him in the chest as he ran into it.

Rodney coughed as the blow took his breath away and he fell over to slide along the floor for several metres. He curled up on the ground and struggled to breathe as it felt like all his ribs had just been broken and his lungs were not co-operating.

He looked up and watched the marine walk away as Evans and Silvestro walked around the corner and came over to him.

Evans crouched down and drew out the knife. He held it threateningly over Rodney, who had only just been able to start breathing again as he lay on the floor.

**"We told you not to try anything! When will you learn that we are in control and there is nothing we will not do to complete our mission."**

Rodney closed his eyes and waited for the knife to be plunged into him. He was more than a little confused when he felt rough hands grabbing him and pulling him up to his feet.

"**Keep moving. We're going to the Jumper Bay,**" Silvestro said.

She suddenly noticed the headset still behind Rodney's ear, reached forwards and grabbed it. She then dropped the tiny device on the floor and Rodney winced as she used her heel to stamp and crush it into the floor.

She still had the roll of duct tape in her hand and Rodney eyed it nervously before he was spun around and shoved onwards.

By the time he entered the transporter, Rodney knew it was now too late to do anything. Not that there was anything he could have done anyway. He felt utterly defeated and alone. Evans grabbed his arms again and twisted them up behind his back so that he could not try and press the map of Atlantis and take them anywhere other than the Jumper Bay.

Silvestro pushed past them and touched the wall display and seconds later they were standing at the edge of the hanger surrounded by Jumpers.

Evans let go of Rodney's arms and pushed him in between the shoulder blades. The impact caught him off balance and Rodney fell forwards and landed with a soft, "Oomph," on the floor outside the transporter.

He rolled over onto his back and grimaced as he stared up at the ceiling. _That's more bruises to add to the list_, he thought sadly. His view was soon obscured by the vacant expressions of his tormentors as they leaned over him and then pulled him upright once more.

They held onto both of his arms tightly so that Rodney could not wriggle free to get away from them. He was manhandled into the rear compartment of a Jumper and shoved forwards brutally until he was in the cockpit. There he was turned and forced to sit down.

Silvestro and Evans walked away from him a short distance, Rodney was unsure why. _Probably to discuss the best way to torture and coerce me to carry out their evil scheme_. He saw his chance and reached forwards to tap the comm.

"Sh-Sheppard?" He muttered quietly.

"_Go ahead McKay."_

Rodney winced at how loud and obvious the communication was, as Sheppard's voice echoed and filled the cockpit.

"John… I… I…" Rodney turned and saw Silvestro had torn a strip of the tape and Evans now had the knife ready in his hand. McKay stood up in the cockpit and tried to put himself in a fighting stance, like he had been shown in training, in a desperate effort to block what was about to happen.

"_Rodney? What is it?"_

Knowing he was about to be defeated and figuring he had nothing to lose, Rodney quickly said, "I'm in the Jumper Bay."

Suddenly Evans lurched forwards and before Rodney could move out of the way or defend himself, Evans stabbed the knife up to the hilt into the side of his left thigh.

He cried out as his legs collapsed under him and he fell down.

Silvestro stepped over him and deactivated the comm. She then crouched down and stuck the tape over his mouth so that he had difficulty in getting enough air as he breathed loudly through his nose.

**Fly the ship and fire the drones into the Gate Room. If you shoot accurately enough to destroy all the control panels and kill everyone maybe you will live to see another day.**

Rodney tried to reply, but the tape over his mouth made it impossible. He could not even cry out as he was pulled upright by both Evans and Silvestro and forced into the pilot's chair again. He furrowed his brow and tried not to move as Evans reached around him and grabbed the hilt of the knife still protruding from his leg.

Rodney wondered whether he was going to twist it and started to shake in fear and pain as the malevolent being controlling the other scientist kept his hand on the hilt. The tremors only made it worse for him as they made the knife shift in his leg.

He reached his shaking hands down and wrapped them around Evans' wrist as tightly as possible to try and prevent him from turning the knife. Instead, Evans pulled the knife out of him and he tilted his head back and would have screamed had he been able. The only sound Rodney could make was muffled by the tape and his nasal breathing increased in volume.

Before he could recover he felt his hands being grabbed and taped securely onto the control sticks of the Jumper and his feet brought back to be taped against the chair. He found that he was unable to move at all except to turn his head, look out of the window and tilt the controls.

He furrowed his brow and closed his eyes as he felt blood draining out of the knife wound in his leg. He hoped it had not cut an artery or he would be dead very soon.

Their work completed, Evans sat next to him and brandished the blood-tinted blade so that Rodney could see it from the corner of his eye and Silvestro sat behind him.

**Fly the ship or die.**

Rodney wished he could speak to try and get himself out of the dangerous situation he was in. He knew now that the Replicators controlling his colleagues were merciless, deadly and unafraid to carry out their plan with whatever actions it took. He thought that they would take their time to kill him if he did not obey, so he flew the Jumper to buy more time until he could figure out what to do.

Rodney set the Jumper to hover close to the Gate Room and realised that his time was up. He could not free his hands or feet to protect himself and he would never fire a drone at the control room. He brought up the HUD using his mental control and saw that there were twenty life signs showing in the Gate Room and Control Room which his captors wanted him to end at the same time as destroying the rooms.

He shook his head and leaned back in the seat, steeling himself for what the reaction of the Replicators was going to be.

Evans leant closer to him and said, "**Fire the drones!"**

Rodney thought, _No I won't do it! You can threaten and hurt me or even kill me and I still won't do it!_

**So be it**, the voice in Rodney's head announced at the same time as Evans drew the knife back and plunged it into the side of his chest. With his hands still tied in front of him and his arms lifted up, he presented an easy target for his captor.

Rodney closed his eyes as blood flowed up into his throat and choked him. It filled his mouth, but with his lips firmly taped together, there was nowhere for it to go, so he coughed and it was forced out of his nose in a gory spray over the controls.

He felt himself weakening as the knife stayed in-between his ribs and he found it hard to breathe through the blood.

**Fire the drone and we will end it.**

Rodney swayed in his seat and was just about to pass out; when Silvestro reached forwards and tore the tape from over his mouth.

Rodney gagged and spat out the blood which made him wince and shudder in disgust.

"No. I'm not going to do it!" Rodney gasped with his eyes screwed tightly closed as more blood dribbled from his mouth.

Evans left the knife embedded in his chest and leant forwards again to get closer to the distressed man, "**You are braver than we thought. You seem to have a disregard for your own well-being and life, but how strong will you be to resist if we kill another?"**

Rodney looked at him in terror and screamed as Evans retrieved the knife from his chest with a savage twist of his hand.

Evans then spun in his chair, got up and stood behind Dr Silvestro, who was still under the influence of the Replicator control and just sat staring blankly at Rodney even as Evans brought the blood-stained knife up to her throat.

Rodney muttered, "Don't kill her. If you want to kill someone, then kill me!"

**Fire the drones and we will not have to.**

Rodney wrenched against the restraints trying desperately to free himself and stop what was about to happen. The pulling motion hurt too much for him to continue and made him whimper in pain as his crimson blood flowed out of his leg and chest and pooled on the floor under him.

He turned away and grimaced as he closed his eyes when he heard a body slump down onto the floor behind him.

He brought up the HUD again as Evans sat back down in the seat next to him with the knife still in his hand. Rodney eyed it nervously and returned his gaze to the sensor readout.

He saw two other Jumpers approaching just before the comm activated, _"Colonel Sheppard to Jumper Ten."_

**If you reply, things will get even worse for you.**

Rodney ground his teeth together in agony and wondered whether things could possibly get much worse for him at the moment.

Evans reached down and grabbed the roll of duct tape which had fallen onto the floor from Silvestro's limp hand. He held it ready and Rodney was only a tiny bit glad when he was not gagged again. He did not think he had the strength left to continue breathing for much longer anyway, let alone only through his nose.

**Shoot them down or they will destroy us.**

Evans brought the tip of the gore soaked blade in close to Rodney's side. He flinched away from the knife, but it caused more agony to course through him and he gave a soft yelp just before he gritted his teeth.

He trusted to the flying skills of the pilots in the other Jumpers and fired the drones to prevent himself from being stabbed again. He really did not think he would survive another knife wound as he could already feel himself rapidly weakening.

"_Lorne break right!"_

"_Acknowledged."_

Rodney made the drones follow the other Jumpers as best he could, but his tired mind soon lost track of them and he eventually saw them disappear off the HUD completely as his strength faltered and he lost control.

"_Lorne?"_

"_I know Sir, it happened to me too. It just stopped, I don't understand it."_

"_Nor do I Major. Converge on Jumper Ten."_

"_Understood."_

Rodney turned his head to look at Evans, who still held the blade dangerously close to McKay's right side. His expression was as vacant as ever.

Rodney looked away and mumbled through the blood tainting his lips, "I don't care what you do to me, I won't kill twenty people and destroy the Gate Room."

He was still looking out of the window when Evans sunk the knife into his side and made Rodney squirm to get away as he cried out weakly.

McKay slumped over the control panel and wished there was some way he could get his hands free to stop the blood leaking from him. Evans pulled the knife out, but Rodney was now too weak to move or make any sound.

Evans reached forwards and got his free hand underneath Rodney's chest. He levered the gravely injured scientist up and back into his chair.

He held the knife in front of Rodney's narrowed eyes and let the blood drip off into the man's lap. **"Fire the drones."**

Rodney mused that maybe he could fire it and pretend it was going to hit the Gate Room, then turn it around to hit an unoccupied building. He hoped that in that time Sheppard would have thought of a way out of the situation, because Rodney was drawing a blank and the blood loss and pain where not aiding his thought processes very well.

He was too weak to realise that there had not been a voice speaking into his head for a while and it did not notice his plan, even though it had been able to read his mind before.

He fired the drone and it streaked out towards the Tower.

He cursed Sheppard as he knew it was him who manoeuvred his craft into the path of the drone before Rodney could correct the course. There was a large explosion which made Rodney close his eyes so that the bright light did not damage them.

"_Colonel?"_

"_I'm fine, but I don't think I'll be doing that again in a hurry."_

Rodney sighed in relief and winced as fresh tremors of pain ran through him from the bleeding wounds in his leg, chest and side.

**"One more shot and you can end it,"** Evans said.

"That's where y-y-you're wrong," Rodney stammered, "I w-w-won't d-d-do it."

Every word was forced out in agony and Rodney finally closed his eyes for the last time as he fell forwards unconscious. He was still taped to the controls and chair so he was unable to slip onto the deck.

Dr Evans suddenly dropped the knife and duct tape and looked bleary eyed around the cockpit at Rodney bound and bleeding slumped over the controls and Dr Silvestro, who was clearly dead, on the floor behind him. He muttered, "Rodney? What the hell's going on? How did I get here?"

Suddenly an explosion rocked the Jumper and Evans was thrown from his seat as the craft lost power and the inertial dampeners went offline. Rodney had not bothered to raise the shields. He hit his head on the deck and lost consciousness.

The Jumper spun down as the engines failed, but was soon stopped in its descent by the grapple hooked onto the hull.

The craft swung rapidly and impacted into a building. Rodney was only saved from being broken by the fact that he was still secured in his seat, but Evans and Silvestro were flung savagely and in a bone-breaking manor as they were tossed around inside the Jumper.

The movement only ceased when the battered Jumper was laid to rest on the pier.

* * *

TBC

A/N – in case you're curious, this was going to be a gratuitous torture tag for Progeny, but something weird happened while I was mapping it…


	4. Aftermath

A/N – Apologies if my medical stuff is incorrect. I'm only here for whumpy fun…

_

* * *

_

_Sheppard and Lorne both deactivated the grapple lines and Sheppard noticed there was still one very faint life sign on the HUD._

"_Son of a…" he muttered, "We need a medical team to meet us on the South Pier."_

_Both of the fully functioning Jumpers landed next to the one they had just shot down as a small plume of smoke leaked out from the wreckage and rose into the Lantean sky above._

_

* * *

_

**Chapter 4 – Aftermath**

Sheppard rushed out of the back of his Jumper, only pausing on the way to wrench the fire extinguisher from the wall in the cockpit and sling the medical kit over his shoulder.

The Jumper he had just shot down was fortunately resting flat on the pier, as what was left of the drive pods kept it level. Major Lorne exited the back of his Jumper with the same gear as Sheppard.

"Colonel, Sir, there's still one life sign on board."

"I saw it too," Sheppard said as he stepped up to the rear hatch of the damaged vessel.

The engine on one side was still smoking and tiny flames were licking at the side of the Jumper's hull. Lorne walked around and doused the fires as best he could with his extinguisher.

He called out, "We need to put out these fires, or get them out of there."

Sheppard nodded and watched as the hatch slowly opened in front of him. He resisted the urge to cough as thick black smoke billowed out and escaped into the air around him. The atmosphere in the Jumper was soon almost clear apart from sporadic puffs of smoke still coming out of sparking circuitry which was hanging down from the ceiling.

He walked inside and took in the scene before him. Two figures were lying on the floor, one had a slit throat and the other was as pale as a ghost. He suddenly realised that they were the same people he had seen in the science lab with Rodney just a short while ago, although the significance of that realisation was lost on him at the moment.

He then reeled a little in shock when he saw a third figure lying face down and unconscious on the control panel. He saw the Canadian flag on the man's arm and braced himself for the worst.

He tapped his radio, "Lorne, I need your assistance."

A moment later, the Major stepped into the Jumper to join him. He whistled before he spoke when he too saw the carnage, "The worst of the fires are out Sir. I think we should be safe for the time being."

Sheppard walked over the female scientist and checked for a pulse or any signs of life; finding none he turned to Lorne and pointed down at the prone figure of the other scientist on the floor, "Help him, while I help Rodney."

Lorne nodded and crouched down while Sheppard walked over to Rodney. He noted in alarm that McKay was taped to the controls and to the chair and was bleeding heavily from numerous injuries.

Sheppard put his hand under Rodney's head and placed it close to the man's nose and mouth. There was blood smeared across his face and shining on his lips and chin. He felt a small breath as it blew across the back of his hand faintly. He quickly grabbed his knife and carefully cut through the bonds. McKay's arms fell down to hang limply by his sides, almost trailing on the floor, but he stayed in his chair with his face turned towards John.

Having no idea how badly Rodney had been hurt and knowing he was still breathing for the time being; Sheppard decided not to move him until Carson could take a look.

He strapped an oxygen mask over the scientist's face from the medical kit and then wrapped pressure bandages around the wounds he was able to see. He pressed one hand against McKay's side and the other to his leg and hoped that Carson would hurry up with his medical team.

He turned to see how Major Lorne was and as his eyes scanned around the cockpit, he noticed a bloody knife and a roll of duct tape on the floor which had been thrown across the cockpit as the craft pitched down. He frowned when he saw Major Lorne doing CPR on the male scientist.

Sheppard reached up with his red and sticky hands and tapped his radio before once again pressing it down against Rodney's side, "Sheppard to Dr Beckett."

"_We're on our way Colonel. What's the situation?"_

"There are three civilians. One has a slit throat, another, well Major Lorne is doing CPR I'm not sure of his condition or the extent of his injuries."

Sheppard turned back to look at the pale and blood streaked face of the man he was trying to save. He steeled himself and prepared for the report on the condition of his friend, "And Rodney. I saw a knife, I think he's been stabbed several times. He's badly bleeding from the chest, side and leg. I'm not sure how long he's been like this. Hurry."

There was a slight pause before Carson spoke, _"We've just left the transporter and we can see the smoke from over here. ETA one minute."_

Sheppard sighed and spoke quietly into McKay's ear, "Hang on Rodney, Carson will be here soon. Don't you die on me before he gets here."

Lorne was still counting out compressions in a whisper behind him and would stop every now and then to give the other scientist breaths.

Sheppard's hands ached from keeping up the pressure and Rodney's blood began to soak through the bandages and through his fingers. McKay's breath was now audible inside the mask in the form of a shallow wheeze.

As Rodney's breathing became quieter and more laboured, Carson rushed into the Jumper with a full medical team in tow.

He looked at the scene and muttered, "Oh my god," before pointing to another Doctor with him to help Major Lorne. He then leant over next to Sheppard to examine Rodney. He expertly inserted IV lines into Rodney's arms and then grabbed his stethoscope to listen to the back of McKay's chest. While he worked, another member of the medical team gently pushed Sheppard away and took his place. She put extra bandages over the ones already on Rodney's side and leg and kept up the pressure.

Sheppard was quite glad that he had been forced away and looked down in shock at his blood soaked hands. There was very little room in the cramped cockpit so he walked away and swept some debris off the bench in the rear compartment before sitting down. Major Lorne joined him a few seconds later and they shared a silent look of worry.

Carson called out behind him, "I need a backboard and a collar and I'm going to have to intubate."

The Doctor with the other scientist called out for a defibrillator.

Carson used his hands to check Rodney and muttered under his breath, "Spine is intact, no obvious limb fractures." As he checked McKay's chest close to the knife wound he stopped and frowned, "One, possibly two broken ribs."

The backboard was lowered down next to the chair and Carson, with help from his team, moved Rodney gently away from the controls and lay him down. Carson quickly and expertly slid a tube into the injured man's mouth and down into his lungs and then they carried him away.

Sheppard turned around to see the other scientists were also on stretchers. The woman had a blanket over her face, but as the man was placed on the waiting gurney outside, the medical staff continued in their efforts to bring him back with CPR even as he was pushed away.

Sheppard was dazed for a moment and Major Lorne spoke, "Come on Sir, let's head over to the infirmary and meet up with Dr Weir and the others."

John nodded and walked out of the wreckage with Major Lorne.

* * *

Dr Beckett came out of surgery looking tired and worried. He looked around at Sheppard, Teyla, Ronon and Dr Weir and said, "I've got Rodney stabilized and repaired as much of the damage as possible. But there was extensive internal bleeding from the knife wounds. Not to mention two broken ribs from where he was stabbed in the chest. There is always a risk we may have missed something and he is very weak."

Sheppard nodded grimly and Dr Weir asked, "What about the others, Dr Silvestro and Dr Evans?"

Carson looked at her sadly, "I'm sorry lass, neither of them made it."

Dr Weir pursed her lips and looked away.

Ronon asked to the gathering in general, "Do you know what happened to him in the Jumper?"

Dr Beckett shook his head, "We got Rodney's blood work back from earlier after the analysis was complete. There was nothing unusual about it." He sighed, "If you'll excuse me, while I'm quietly confident that Rodney's usual stubbornness will hold fast and pull him through, it could still go either way. I need to keep monitoring him just in case. He's too weak for you to see him at the moment, but I'll call you back later."

Elizabeth looked up and said, "Of course."

Sheppard said, "Rodney had been acting strangely ever since we went into the Ancient building on our mission this morning."

Teyla frowned, "That is true, but why would he not ask us for help if he were in trouble?"

Ronon grunted in agreement, "What about the video feeds?"

Sheppard nodded, "Maybe they can shed some light on exactly what's been going on over the last few hours to have culminated in this."

Sheppard tapped his radio and asked Zelenka to meet him in the Briefing Room in five minutes.

* * *

They all sat in the Briefing Room and watched Rodney's strange conversation with his staff. Sheppard winced when Rodney said he had been feeling 'heart attack inducing pain.' He wished McKay had told him something, _anything_ about what was going on. Maybe then he would not be lying in the infirmary fighting for his life.

They continued to watch and Zelenka switched the feed to follow Rodney as he went to his quarters. He fast-forwarded and they saw the scientist leave his room and head back to the lab.

Sheppard noticed the gun now strapped to Rodney's leg and sighed. He had failed again in that respect. McKay had obviously known he was in danger and Sheppard had blithely and unknowingly stripped him of his only protection.

They watched him go into the lab and sit down. Zelenka again skipped the video on a few hours until Rodney started talking. They listened tensely as he spoke about Replicators and how they wanted to destroy Atlantis.

They all flinched and Ronon growled as Rodney was pushed down onto the ground and hit the table. Sheppard had to restrain himself from jumping out of his seat in fury as the two scientists assaulted Rodney as he stood defenceless and trapped with his arms behind his back.

Sheppard then grimaced when he saw his own conversation with Rodney, where it was now so obvious he was in pain and deep trouble. It made Sheppard feel a crushing weight of guilt over why he had not forced Rodney to come with him back to the infirmary straight away.

Weir looked over at Sheppard with a sad face and indicated for them to continue watching before anyone said anything.

Teyla gasped when she saw Rodney run into the fist in the corridor and collapse.

Sheppard reached up and tapped his radio, "Major Lorne, I want you to locate and escort Corporal Harvey to the brig."

They saw Rodney leave the transporter and get pushed onto the floor. They eventually lost him as he entered the Jumper. Most of the rest they would need to analyse the logs from the Jumper or wait for Rodney to wake up and tell them.

A stunned silence filled the Briefing Room when Zelenka shut down the video feed.

Radek looked down at his laptop blankly and muttered, "How is Rodney? I heard he had been hurt, but I had no idea."

Elizabeth turned to him, "He's in a bad way, but Carson's with him."

They were about to start discussing the video they had just seen, when Elizabeth's radio activated, _"Beckett to Dr Weir."_

She held up her hand to the others and replied, "Go ahead Carson."

"_I've found something you'll want to see. Dr Zelenka too."_

She looked up at Radek, "He's here with me now, we'll be right there."

She stood up and left with the others all following her.

* * *

Rodney's team, with Zelenka and Weir stood crowded around Dr Beckett in his lab.

He was studying some data on his screen and frowned as he looked up at the people gathered around him who were watching in expectation.

He said, "We managed to get a blood sample from Rodney, although it was difficult to find any of his original blood left in him after such injuries and so many transfusions. I also obtained blood samples from Dr Evans and Dr Silvestro."

Beckett pushed himself away from the desk and stood up before he said, "Dr Zelenka I think you need to see this."

Radek walked over and peered at the screen. He pushed his glasses up and sat down to analyse the three blood test results displayed on the screen. He typed and few keys and frowned.

"They are definitely Replicator nanites." He continued to type for a few more minutes and then spoke again, "They are completely inert. I believe they have run out of power, which is unusual for Replicator cells, unless they wanted to be completely separate from the host. That would explain it, as they would not be able to draw any energy from the surrounding tissue to stay operational for long."

Dr Weir frowned, "Are they still a danger to us?"

Zelenka looked up from the data, "I do not believe so, but I will need to analyse this data in more detail."

Dr Beckett said, "I will need to take blood samples from everyone on the base to make sure all the nanites are deactivated just in case they spread to anyone else. I will see if I can develop a method for removing them from the bloodstream as well."

Elizabeth nodded, "Good work and keep me apprised."

Ronon asked Beckett, "Can we see McKay yet?"

Carson replied, "Yes, I checked him. He's still very ill, so only for a few minutes please."

* * *

The team shuffled in quietly around Rodney's bed in the intensive care area of the infirmary. John thought McKay looked dead. If it were not for the steady and slow beep of the heart monitor and the sigh of the ventilator he would have thought his assumption was correct.

Rodney's whole chest, abdomen and upper leg were wrapped in white bandages which almost blended in with his pale complexion. There was dark purple bruising around both of his wrists.

Images of Rodney thrashing and struggling against the restraints trying desperately to free himself while he was being stabbed with the knife flashed through Sheppard's mind and made him wince.

Teyla reached down and gently grasped Rodney's left hand, careful not to disturb the IV line, she threaded her fingers through his and said quietly, "You are very brave Rodney and we are most grateful that you did not do as they wanted."

_He paid for that bravery with his blood_, Sheppard thought as he smiled at Teyla sadly. He found that he could not say anything in front of his team as he still felt guilty about letting this happen to Rodney at all.

John stayed for a little longer after the rest of his team left with Dr Weir. He leant forwards close to Rodney's deathly pale face and whispered, "I'm _so_ sorry Rodney, but I'll make it up to you, I promise. But only if you keep fighting and live."

He was saddened when there was no response from the scientist, who just lay completely still with his eyes closed. He patted Rodney's shoulder gently and left to head down to the brig and speak with Corporal Harvey.

* * *

"I swear it, Sir. I don't remember anything," Corporal Harvey said to Sheppard as he stood to attention behind the forcefield in the brig.

John was still unable to believe what he was hearing, "You assaulted a civilian, Corporal and the head of the science department no less. There are serious repercussions for such an act."

Harvey glared back at him, "I do not remember hitting Dr McKay as you are accusing me Colonel, Sir."

Sheppard frowned as he remembered something about Ancient gene carriers from the video feed he watched earlier. He looked back up at the Corporal's face. He was still standing stiffly to attention and not daring to glance at Sheppard.

John knew the man did not have the gene and suddenly remembered that this meant he could have been controlled like the two scientists who kidnapped and tortured Rodney.

He snapped his eyes back up at Harvey, "At ease Corporal. Dr Beckett will be down soon to take a blood sample. I'm going to keep you in here until he's given us the all clear."

Harvey looked a little confused and only slightly relaxed his stance when Sheppard walked away.

* * *

Sheppard spent the rest of the day co-ordinating the blood tests for Dr Beckett. He figured the man had enough on his plate, what with Rodney not being fully out of the woods and having to analyse all the tests.

John then went and sat next to Rodney in the infirmary. He stayed for such a long time that he nodded off and nearly fell out of his seat. One of the nurses set him up with a bed so that he could stay there and be the first to hear any news about his friend.

Dr Beckett also stayed up most of the night working on the blood samples in his lab. He found that everyone on Atlantis had trace amounts of nanites in their blood streams and he was very glad that Zelenka was also helping him and kept reassuring him that every sample he had tested the nanites were out of power and no threat.

Zelenka also advised him that the nanites were beginning to break down when they studied another more recent sample taken from Rodney. He could not explain how or why the tiny machines were disappearing from his system. He suggested it may have been in an attempt to make their attack undetectable after it was over. "Perhaps they were going to try and make it look like Rodney had lost it completely and destroyed us using his own free will," Beckett had muttered darkly during one of their conversations.

Rodney rejected the ventilator the next day as he started breathing on his own. Carson told everyone that he was making excellent progress and should be fully awake in a day or two.

* * *

Sheppard sat with Rodney as much as he could and smiled as he saw some of the colour returning to his face.

His head was lolling to the side as he drifted off to sleep when he was woken up suddenly by a noise from the man lying on the bed in front of him.

Rodney was muttering in panic, "The Replicators! They're controlling everyone they're going to kill me unless I kill everyone else. Oh no no no! One of them has a knife and he says I can't even ask Sheppard for help…"

The rest diminished down into an incoherent whimper and Sheppard stood up and gripped McKay's shoulders as he rode through the nightmare.

He spoke gently, "You're safe Rodney. They've gone. I'm here."

McKay's eyes opened slowly and looked up at Sheppard. They were unfocused and soon closed again as Rodney fell asleep.

Sheppard sighed in frustration and sat back down in his chair.

* * *

Another whole day later, Rodney began to fully wake up. Carson kept checking on him, but he was too traumatised to say anything.

Sheppard still sat next to him as he gazed wide-eyed and fearfully up at the ceiling.

John could not stand it for very long and decided he needed to say something after they had sat like it for half an hour.

"Rodney, you should've said something to us. There were so many opportunities."

McKay tilted his face away from the ceiling towards John and closed his eyes, "I-I-I tried, but you didn't seem to realise. I couldn't say anything directly, but I thought even you would've been able to figure out something wasn't right." He opened his eyes and looked at John, "They threatened to kill you if I said anything."

"And they very nearly killed _you_ instead."

"At least I knew what was going on and saw it coming. I couldn't let them do that to you."

Sheppard smiled at him, "Thanks Rodney, but I am able to defend myself and it's my job to protect you. I hope you never hide something like this from me again."

Rodney mistook his tone as berating and sighed sadly as he turned his gaze back up to stare at the ceiling once more.

Sheppard frowned and asked, "So what happened on the Jumper? We tried to reconstruct the logs, but Zelenka said they were too badly damaged."

Rodney sighed and winced as his broken ribs shifted slightly. He closed his eyes and mumbled, "I don't want to talk about it. Not yet."

Sheppard patted his friend's shoulder, "That's okay, we'd just like to know what happened to Dr Evans and Dr Silvestro."

A frown creased Rodney's forehead. He knew that both scientists were dead, but did not realise he was the only one who had been present and knew how they had died. He felt he owed it to them to tell someone exactly what had happened so that their deaths would not be meaningless.

He steeled his nerve and began to speak. He felt a weight lifting from his chest as he finally told someone else exactly what had happened to him in the fated Jumper. The craft now lay in pieces in the Jumper Bay, where Zelenka was trying to repair it.

Rodney slowly recounted everything that happened to him. He furrowed his brow and closed his eyes as he told Sheppard about how he was tied up and brutally stabbed whenever he did not do as the Replicators asked.

Sheppard felt proud at how much Rodney had been able to endure before he was finally broken and fired the drone towards the Control Room.

He was therefore quite shocked to find out that Rodney had not actually broken at all and he was going to send the drone off course at the last moment even if it meant he would be stabbed again and probably die.

Rodney said, "I only fired it to give you time to think of a way out of the situation. It's a shame your solution involved shooting my Jumper out of the sky."

Sheppard replied, "Well it was the only thing I could come up with in the time you gave me."

A long silence filled the air after Sheppard spoke and he thought Rodney had drifted off to sleep.

He was therefore surprised when Rodney spoke tiredly, still with his eyes closed, "You know what John? I do feel better now, I'm glad you made me tell you what happened. I don't think I would have been able to survive for much longer with something like that buried in my memories."

Sheppard smiled as he looked into McKay's pale face. He knew it would take time. Rodney had been returned to them damaged, but certainly not broken and he would eventually learn to deal with the memories and the scars.

* * *

The End

A/N – This was going to be a two part Puddle Jumper Mayhem story. Wasn't I surprised when it turned into this! Thanks for reading (and for the reviews) x Varda x


End file.
